[Biophp-dev] Brief update - No, I'm not dead...

S Clark biophp-dev@bioinformatics.org
Fri, 3 Oct 2003 12:10:28 -0600

Hash: SHA1

Work issues have been keeping me thoroughly distracted, but not only have I
not been totally inactive, I've actually gotten some work done on BioPHP co=

I got my first chance to use BioPHP code for a 'real-world' project, and was
pleased to see that the BLAST frontend and parser still worked (NCBI had
evidently modified their web interface somewhat, but as the BioPHP BLAST
interface to their system uses XML mode output instead of "screen scraping"
it was unaffected).

Additionally, I was able to get the local blast frontend written and workin=
I'm very glad I separated the results parser from the frontend code - it wo=
unchanged with the XML output from local blast as well as the NCBI "URLAPI"
interface results.

I have one set of additions that I want to make before posting the code.=20
Currently, both modules have a direct but somewhat unintuitive couple
of interface methods for setting the search parameters.  I intend to
add a set of identically-named interface methods to both frontends
so that the same (more intuitive) commands can be used to set
the BLAST query parameters for either one.

If there is anyone who doesn't want to wait for me to do this, please
speak up - I have no problem posting the code as it is if anyone
is interested in it (and I will not be removing the less-intuitive
'core' parameter setting method, so the updated versions will not
break any scripts written to use them).

I have unfortunately not had much time to work on the 'core seq object
re-implementation'.  Is anyone interested in looking at the layout I've
got currently to make comments or suggestions (or just to work on them)?

On a final note, Serge has mentioned that his classes are nearly over, so=20
he should be returning soon.  We may be seeing a flood of code updates=20
at the GenePHP site soon! (Welcome back, Serge!)

Thanks, everyone, and as always, any comments, suggestions, or requests
are welcome here.

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